[gmx-users] image centering

[Alan Dodd]

Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result?  I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other.  What does the output look like when you use the option -centre?  If nothing else, seperating the commands might help you find the source of the problem.


----- Original Message ----
From: Myunggi Yi <myunggi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, December 25, 2007 9:48:29 PM
Subject: [gmx-users] image centering

Dear users,

I have a membrane simulation trajectory,
in which the solvent (water and ions) is separated by lipid bilayer.

I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell. 

I have tried the followings.

trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster
trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole

Both pbc and center didn't work.
Is there any way to center the solvent?

Happy holidays.


-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics 
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi


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